Double mutant analysis.¶

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['Aminoacid mutation in partner 1', 'Aminoacid mutation in partner 2', 'mean enrich tandem mutant', 'stdev', 'median', 'quant_1st ', 'quant_2nd', 'mean1 vs WT', 'stdev1', 'median1', 'quant_1st1', 'quant_2nd1', 'mean2 vs WT', 'stdev2', 'median2', 'quant_1st2', 'quant_2nd2', 'size in terms of number of bc', 'size1', 'size2']
Total number of mutations expected in p1: 185
Number of mutations observed in p1: 117
Total number of mutations expected in p2: 190
Number of mutations observed in p2: 102
Out[2]:
Aminoacid mutation in partner 1 Aminoacid mutation in partner 2 mean enrich tandem mutant stdev median quant_1st quant_2nd mean1 vs WT stdev1 median1 quant_1st1 quant_2nd1 mean2 vs WT stdev2 median2 quant_1st2 quant_2nd2 size in terms of number of bc size1 size2
0 S30D R32D 1.15 0.19 1.18 0.96 1.31 1.13 0.20 1.16 1.01 1.26 1.10 0.16 1.09 0.98 1.19 5.0 38.0 61.0
1 S30D R32E 0.85 0.52 NaN NaN NaN 1.13 0.20 1.16 1.01 1.26 0.87 0.40 1.03 0.31 1.19 3.0 38.0 39.0
2 S30D R32F 0.82 0.07 0.82 0.75 0.89 1.13 0.20 1.16 1.01 1.26 0.77 0.15 0.79 0.69 0.86 4.0 38.0 71.0
3 S30D R32G 1.12 0.00 NaN NaN NaN 1.13 0.20 1.16 1.01 1.26 0.98 0.12 0.96 0.88 1.05 1.0 38.0 19.0
4 S30D R32K 1.19 0.00 NaN NaN NaN 1.13 0.20 1.16 1.01 1.26 0.99 0.20 0.93 0.84 1.13 1.0 38.0 23.0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
9044 F103V S81F 0.10 0.00 NaN NaN NaN 0.22 0.03 NaN NaN NaN 0.18 0.06 0.17 0.13 0.2 1.0 2.0 58.0
9045 F103V Q88K 0.13 0.00 NaN NaN NaN 0.22 0.03 NaN NaN NaN 0.95 0.18 0.95 0.85 1.03 1.0 2.0 27.0
9046 F103V K90N 0.00 0.00 NaN NaN NaN 0.22 0.03 NaN NaN NaN 0.11 0.03 0.11 0.09 0.12 1.0 2.0 26.0
9047 F103V N92S 0.77 0.00 NaN NaN NaN 0.22 0.03 NaN NaN NaN 1.09 0.15 1.04 1.01 1.17 1.0 2.0 22.0
9048 F103V S95T 0.31 0.00 NaN NaN NaN 0.22 0.03 NaN NaN NaN 0.97 0.25 1.03 0.85 1.14 1.0 2.0 51.0

9049 rows × 20 columns

Useful functions¶

Global analysis of the tandem mutations¶

Number of mutations in partner 1: 117
Number of mutations in partner 2: 102
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Barplots of the individual mutations against WT barcodes for Partner 1¶

Barplots of the individual mutations against WT barcodes for Partner 2¶

In [ ]:

Specific analysis between pairs of residue¶

Mutated AA in partner 1:
 {'F103', 'W33', 'E50', 'N31', 'Y35', 'L56', 'I57', 'R98', 'S99', 'S101', 'T53', 'S30', 'N54', 'Y32', 'N74'}
Mutated AA in partner 2:
 {'T89', 'E135', 'L75', 'N137', 'S95', 'N92', 'Q88', 'I97', 'K90', 'T77', 'E146', 'R32', 'T79', 'S81', 'S147'}

Define below the index of the residues to analyze¶

Number of mutations in partner 1: 10
Number of mutations in partner 2: 11
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color 132

Vizualisation (VHH2-W33 en interaction avec TNF-N92)¶

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Vizualisation (VHH2-S30 en interaction avec TNF-S147)¶

Number of mutations in partner 1: 9
Number of mutations in partner 2: 6
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color 70

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

En fait il faut considérer une autre chaine TNF du trimère¶

Cela démontre la formation du trimère¶

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Vizualisation (VHH2-S101 en interaction avec TNF-T89)¶

Number of mutations in partner 1: 8
Number of mutations in partner 2: 6
0
color 63

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Asking for 2 positions (Par exemple VHH2 S30N - TNFE35S)¶

Number of mutations in partner 1: 117
Number of mutations in partner 2: 102
Mutated AA in partner 1:
 {'F103', 'W33', 'E50', 'N31', 'Y35', 'L56', 'I57', 'R98', 'S99', 'S101', 'T53', 'S30', 'N54', 'Y32', 'N74'}
Mutated AA in partner 2:
 {'T89', 'E135', 'L75', 'N137', 'S95', 'N92', 'Q88', 'I97', 'K90', 'T77', 'E146', 'R32', 'T79', 'S81', 'S147'}

Number of mutations in partner 1: 8
Number of mutations in partner 2: 6
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color 63

Interaction avec une unité du trimère

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Interaction avec l'autre unité du trimère

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Analysis taking into account WT values¶

Analysis of the rescues for individually affected mutations¶

Number of mutations in partner 1: 117
Number of mutations in partner 2: 102
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Analysis taking into account WT values¶

Analysis of highly stabilized pairs for individually favorable mutations¶

Number of mutations in partner 1: 117
Number of mutations in partner 2: 102
0
In [ ]:
In [ ]: